BioC 3.4: CHECK report for RCy3 on malbec1

Package: RCy3

Version: 1.5.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.5.2.tar.gz

StartedAt: 2017-04-15 00:46:32 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:47:22 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 50.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RCy3.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.5.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RCy3.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘1.5.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.BBSOverride: no visible global function definition for ‘as’
is.classic.graph: no visible global function definition for ‘is’
is.multiGraph: no visible global function definition for ‘is’
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘copyCytoscapeNetwork’ ‘renameCytoscapeNetwork’ ‘selectAllEdges’
  ‘selectAllNodes’
Undocumented S4 methods:
  generic 'copyCytoscapeNetwork' and siglist 'CytoscapeWindowClass'
  generic 'renameCytoscapeNetwork' and siglist 'CytoscapeWindowClass'
  generic 'selectAllEdges' and siglist 'CytoscapeWindowClass'
  generic 'selectAllNodes' and siglist 'CytoscapeWindowClass'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RCy3.Rcheck/00check.log’
for details.

* installing *source* package ‘RCy3’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RCy3)

name	user	system	elapsed
CytoscapeConnection	0	0	0
CytoscapeConnectionClass-class	0	0	0
CytoscapeWindow	0.004	0.000	0.000
CytoscapeWindowClass-class	0.000	0.000	0.001
addCyEdge	0.000	0.000	0.001
addCyNode	0	0	0
addGraphToGraph	0.000	0.000	0.001
clearSelection	0.000	0.000	0.001
copyVisualStyle	0.000	0.004	0.001
createWindow	0.000	0.000	0.001
createWindowFromSelection	0	0	0
cy2.edge.names	0.004	0.000	0.000
cyPlot	0.000	0.000	0.001
deleteAllWindows	0	0	0
deleteEdgeAttribute	0.000	0.000	0.001
deleteNodeAttribute	0.000	0.000	0.001
deleteSelectedEdges	0	0	0
deleteSelectedNodes	0	0	0
deleteWindow	0.000	0.000	0.001
demoSimpleGraph	0.000	0.000	0.001
displayGraph	0	0	0
dockPanel	0	0	0
eda	0.004	0.000	0.001
eda.names	0.000	0.000	0.001
existing.CytoscapeWindow	0.000	0.000	0.001
fitContent	0.000	0.000	0.001
fitSelectedContent	0	0	0
floatPanel	0.000	0.000	0.001
getAdjacentEdgeNames	0.000	0.000	0.001
getAllEdgeAttributes	0.000	0.000	0.001
getAllEdges	0	0	0
getAllNodeAttributes	0.000	0.000	0.001
getAllNodes	0.000	0.000	0.001
getArrowShapes	0	0	0
getAttributeClassNames	0	0	0
getCenter	0.004	0.000	0.000
getDefaultBackgroundColor	0.000	0.000	0.001
getDefaultEdgeReverseSelectionColor	0.000	0.000	0.001
getDefaultEdgeSelectionColor	0.000	0.000	0.001
getDefaultNodeReverseSelectionColor	0	0	0
getDefaultNodeSelectionColor	0	0	0
getDirectlyModifiableVisualProperties	0	0	0
getEdgeAttribute	0.004	0.000	0.001
getEdgeAttributeNames	0	0	0
getEdgeCount	0	0	0
getFirstNeighbors	0.004	0.000	0.001
getGraph	0.000	0.000	0.001
getGraphFromCyWindow	0.000	0.000	0.001
getLayoutNameMapping	0	0	0
getLayoutNames	0	0	0
getLayoutPropertyNames	0.000	0.000	0.001
getLayoutPropertyType	0.004	0.000	0.000
getLayoutPropertyValue	0.000	0.000	0.001
getLineStyles	0.000	0.000	0.001
getNodeAttribute	0.000	0.000	0.001
getNodeAttributeNames	0	0	0
getNodeCount	0	0	0
getNodePosition	0	0	0
getNodeShapes	0.004	0.000	0.001
getNodeSize	0.000	0.000	0.001
getSelectedEdgeCount	0.000	0.000	0.001
getSelectedEdges	0	0	0
getSelectedNodeCount	0	0	0
getSelectedNodes	0.000	0.000	0.001
getViewCoordinates	0.000	0.000	0.001
getVisualStyleNames	0	0	0
getWindowCount	0	0	0
getWindowID	0.004	0.000	0.000
getWindowList	0.000	0.000	0.001
getZoom	0	0	0
hideAllPanels	0	0	0
hideNodes	0	0	0
hidePanel	0	0	0
hideSelectedEdges	0.000	0.000	0.001
hideSelectedNodes	0.000	0.000	0.001
initEdgeAttribute	0	0	0
initNodeAttribute	0	0	0
invertEdgeSelection	0.004	0.000	0.000
invertNodeSelection	0.000	0.000	0.001
layoutNetwork	0	0	0
lockNodeDimensions	0.004	0.000	0.001
makeRandomGraph	0.000	0.000	0.001
makeSimpleGraph	0.000	0.000	0.001
noa	0	0	0
noa.names	0	0	0
ping	0	0	0
pluginVersion	0.004	0.000	0.000
predictTimeToDisplayGraph	0.000	0.000	0.001
raiseWindow	0	0	0
redraw	0.004	0.000	0.001
restoreLayout	0.000	0.000	0.001
saveImage	0	0	0
saveLayout	0	0	0
saveNetwork	0	0	0
selectEdges	0.000	0.000	0.001
selectFirstNeighborsOfSelectedNodes	0.000	0.000	0.001
selectNodes	0.000	0.000	0.001
sendEdges	0	0	0
sendNodes	0	0	0
setCenter	0.000	0.000	0.001
setDefaultBackgroundColor	0.000	0.000	0.001
setDefaultEdgeColor	0.000	0.000	0.001
setDefaultEdgeFontSize	0	0	0
setDefaultEdgeLineWidth	0	0	0
setDefaultEdgeReverseSelectionColor	0.000	0.000	0.001
setDefaultEdgeSelectionColor	0.004	0.000	0.001
setDefaultEdgeSourceArrowColor	0.000	0.000	0.001
setDefaultEdgeTargetArrowColor	0.000	0.000	0.001
setDefaultNodeBorderColor	0	0	0
setDefaultNodeBorderWidth	0	0	0
setDefaultNodeColor	0	0	0
setDefaultNodeFontSize	0.004	0.000	0.001
setDefaultNodeLabelColor	0.000	0.000	0.001
setDefaultNodeReverseSelectionColor	0.000	0.000	0.001
setDefaultNodeSelectionColor	0	0	0
setDefaultNodeShape	0.000	0.000	0.002
setDefaultNodeSize	0	0	0
setEdgeAttributes	0.000	0.000	0.001
setEdgeAttributesDirect	0.000	0.000	0.001
setEdgeColorDirect	0	0	0
setEdgeColorRule	0.000	0.000	0.001
setEdgeFontSizeDirect	0.000	0.000	0.001
setEdgeLabelColorDirect	0.000	0.000	0.001
setEdgeLabelDirect	0	0	0
setEdgeLabelOpacityDirect	0.000	0.000	0.001
setEdgeLabelRule	0.000	0.000	0.001
setEdgeLineStyleDirect	0.000	0.000	0.001
setEdgeLineStyleRule	0.000	0.000	0.001
setEdgeLineWidthDirect	0.000	0.000	0.001
setEdgeLineWidthRule	0	0	0
setEdgeOpacityDirect	0.000	0.000	0.001
setEdgeOpacityRule	0.000	0.000	0.001
setEdgeSourceArrowColorDirect	0.000	0.000	0.001
setEdgeSourceArrowColorRule	0.000	0.000	0.001
setEdgeSourceArrowOpacityDirect	0.004	0.000	0.001
setEdgeSourceArrowRule	0	0	0
setEdgeSourceArrowShapeDirect	0.000	0.000	0.001
setEdgeTargetArrowColorDirect	0	0	0
setEdgeTargetArrowColorRule	0.000	0.000	0.001
setEdgeTargetArrowOpacityDirect	0.004	0.000	0.001
setEdgeTargetArrowRule	0.000	0.000	0.001
setEdgeTargetArrowShapeDirect	0	0	0
setEdgeTooltipDirect	0.000	0.000	0.001
setEdgeTooltipRule	0.000	0.000	0.001
setGraph	0	0	0
setLayoutProperties	0.000	0.000	0.001
setNodeAttributes	0.000	0.000	0.001
setNodeAttributesDirect	0	0	0
setNodeBorderColorDirect	0.000	0.000	0.001
setNodeBorderColorRule	0	0	0
setNodeBorderOpacityDirect	0.004	0.000	0.001
setNodeBorderWidthDirect	0.000	0.000	0.001
setNodeBorderWidthRule	0	0	0
setNodeColorDirect	0	0	0
setNodeColorRule	0.000	0.000	0.001
setNodeFillOpacityDirect	0.000	0.000	0.001
setNodeFontSizeDirect	0.000	0.000	0.001
setNodeHeightDirect	0	0	0
setNodeImageDirect	0	0	0
setNodeLabelColorDirect	0	0	0
setNodeLabelDirect	0.000	0.000	0.001
setNodeLabelOpacityDirect	0.000	0.000	0.001
setNodeLabelRule	0.000	0.000	0.001
setNodeOpacityDirect	0.000	0.004	0.000
setNodeOpacityRule	0	0	0
setNodePosition	0.000	0.000	0.001
setNodeShapeDirect	0.004	0.000	0.001
setNodeShapeRule	0.000	0.000	0.001
setNodeSizeDirect	0.000	0.000	0.001
setNodeSizeRule	0.004	0.000	0.001
setNodeTooltipRule	0.000	0.000	0.001
setNodeWidthDirect	0.000	0.000	0.001
setTooltipDismissDelay	0.000	0.000	0.001
setTooltipInitialDelay	0.000	0.000	0.001
setVisualStyle	0	0	0
setWindowSize	0.000	0.000	0.002
setZoom	0.000	0.000	0.001
showGraphicsDetails	0.004	0.000	0.000
unhideAll	0	0	0